An error occurred in the fp step using cp2k #1223
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Question 1:According to the tutorial, I used the init_bulk module to generate POSCAR files with only two C atoms. Does this make sense as the initial data?
Question 2:I had an error running the dpgen to fp step
The error:nohup: ignoring input
/opt/mamba/lib/python3.10/site-packages/gromacs/init.py:286: GromacsImportWarning: Some Gromacs commands were NOT found; maybe source GMXRC first? The following are missing:
['release']
warnings.warn("Some Gromacs commands were NOT found; "
INFO:dpgen:-------------------------iter.000000 task 01--------------------------
INFO:dpgen:-------------------------iter.000000 task 02--------------------------
INFO:dpgen:-------------------------iter.000000 task 03--------------------------
INFO:dpgen:-------------------------iter.000000 task 04--------------------------
INFO:dpgen:-------------------------iter.000000 task 05--------------------------
INFO:dpgen:-------------------------iter.000000 task 06--------------------------
INFO:dpgen:system 000 candidate : 23 in 8040 0.29 %
INFO:dpgen:system 000 failed : 28 in 8040 0.35 %
INFO:dpgen:system 000 accurate : 7989 in 8040 99.37 %
INFO:dpgen:system 000 accurate_ratio: 0.9937 thresholds: 1.0000 and 1.0000 eff. task min and max -1 30 number of fp tasks: 23
Traceback (most recent call last):
File "/opt/mamba/bin/dpgen", line 8, in
sys.exit(main())
File "/opt/mamba/lib/python3.10/site-packages/dpgen/main.py", line 185, in main
args.func(args)
File "/opt/mamba/lib/python3.10/site-packages/dpgen/generator/run.py", line 3642, in gen_run
run_iter (args.PARAM, args.MACHINE)
File "/opt/mamba/lib/python3.10/site-packages/dpgen/generator/run.py", line 3625, in run_iter
make_fp (ii, jdata, mdata)
File "/opt/mamba/lib/python3.10/site-packages/dpgen/generator/run.py", line 2827, in make_fp
make_fp_cp2k(iter_index, jdata)
File "/opt/mamba/lib/python3.10/site-packages/dpgen/generator/run.py", line 2686, in make_fp_cp2k
cp2k_input = make_cp2k_input(sys_data, fp_params)
File "/opt/mamba/lib/python3.10/site-packages/dpgen/generator/lib/cp2k.py", line 159, in make_cp2k_input
update_dict(default_config, user_config)
File "/opt/mamba/lib/python3.10/site-packages/dpgen/generator/lib/cp2k.py", line 69, in update_dict
if (k in old_d and isinstance(old_d[k], dict) and isinstance(update_d[k], collections.Mapping)):
AttributeError: module 'collections' has no attribute 'Mapping'
my param.json :
"ratio_failed": 0.20,
"fp_style": "cp2k",
"shuffle_poscar": false,
"fp_task_max": 30,
"fp_task_min": 1,
"fp_pp_path": ".",
"fp_pp_files": [],
"user_fp_params": {
"FORCE_EVAL":{
"DFT":{
"BASIS_SET_FILE_NAME": "BASIS_MOLOPT",
"POTENTIAL_FILE_NAME": "GTH_POTENTIALS"
},
"SUBSYS":{
"KIND":{
"_": ["C"],
"POTENTIAL": ["GTH-PBE-q4"],
"BASIS_SET": ["DZVP-MOLOPT-GTH"]
my machine.json :
"fp":
[{
"command": "mpirun --allow-run-as-root --oversubscribe /root/cp2k-7.1/exe/local/cp2k.popt -i input.inp",
"machine": {
"batch_type": "Lebesgue",
"context_type": "LebesgueContext",
"local_root" : "./",
"remote_profile":{
"email": "",
"password": "",
"program_id": ,
"keep_backup":true,
"input_data":{
"job_type": "indicate",
"log_file": "task*/fp.log",
"grouped":true,
"job_name": "dpgen_fp_job",
"disk_size": 100,
"checkpoint_files": "sync_files",
"checkpoint_time":30,
"scass_type":"c16_m32_cpu",
"platform": "ali",
"image_name":"LBG_CP2K_7.1_v1",
"on_demand":0
}
}
},
"resources": {
"number_node": 1,
"cpu_per_node": 4,
"gpu_per_node": 0,
"queue_name": "F1_4_0",
"group_size": 3,
"source_list": ["/opt/intel/oneapi/setvars.sh","/root/cp2k-7.1/tools/toolchain/install/setup"]
}
}
]
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